What has happened is absolutely normal. You can't go from Green to Gold. You have to go to Silver first, and this resets your Club Miles to zero. It's the way it always has been.

The only issue is, as cxfan1960 says, that the upgrade batch only runs once a day and both your AA flights posted together so you "lost" 14,000 miles when you should have only lost about 6,400, and have 7,000 Club Miles towards Gold qualification. This seems like reasonable grounds for complaint to me. I would write to CX Customer Relations and point out that the unreasonableness of what happened.

And for future reference, CX bases everything on posting date, so what you could have done in your case was to remove your MPC number from the second flight AA289, wait for the first flight to post, which would have triggered the upgrade to Silver, then submitted a missing mileage request for the second flight.

Having said all that, if they do upgrade you to Gold at 48,000 miles then you will have got a better result even than you would have got by the two flights posting separately.